Yeah its not terribly difficult, just use a blade razor and work one side at a time. You shouldn't need to separate the glass unless its visibly bad below the mess you got there.
Take your time with it, its not unlike caulking a shower stall.
No, not terribly difficult...but let's be honest, it is a tedious, pains-taking, time-consuming task that is not particularly enjoyable. Especially if it is the OP's first time doing it; he must be super careful not to damage that structural seal between glass panels. There's an art to it that must be learned. He needs to cut down through the old seal holding the blade flat against the pane of glass that is butted up against the other side; if he runs the blade along the wrong panel he risks cutting into the structural seal between panes. After the initial cut, he needs to hold the blade at a high enough angle that the first pane prevents it from slipping into that crevice while scraping the silicone off the second pane. And he's got to get it all off...every last trace.
Applying the silicone at the end is the easy part, and is indeed similar to caulking a shower stall or bathtub. But the preparatory removal of the old stuff is the hard part, and it's not a job to jump into without knowing that you are committed.
OP, I'm not saying that you shouldn't do it; just think it through carefully before starting.
